Hoyo Negro skeleton mtDNA

For those of you who haven't been keeping up on cave archaeology in Mesoamerica, a remarkably complete skeleton of late Pleistocene girl was discovered deep underwater in a cave near Tulum, Quintana Roo, a couple of years ago. Reports of skeletons and other artifacts in similar contexts have been floating around for years. Most of us presumed, I think, that these remains were quite early because the caves were flooded by post-Pleistocene sea-level rise. The cave near Tulum was named Hoyo Negro, and the remains of the young woman were nicknamed Naia. In 2014, her mtDNA sequence was reported along with dates suggesting the skeleton was 12,000 to 13,000 years old (1).

In today's issue of Science, Kay Prufer and Matthias Meyer of the Max Planck Institute for Evolutionary Anthropology argue in a comment (2) on the original article that mtDNA haplotype was incorrectly identified and was came from modern contamination because it did not show the level and type of damage they would have predicted.

The response (3) is robust. While conceding that the lack of damage to parts of the DNA sequence is perhaps unexpected, they argue that damage to ancient DNA is poorly understood and unpredictable. Therefore, it cannot be used by itself to prove or disprove that a particular sequence or segment of DNA is ancient. They also provide a reasonably compelling argument against contamination.

Both the comment and the response discussed whether and how DNA might be damaged  in different environments, including the tropical environment of Quintana Roo. What surprised me was the lack of any explicit consideration of the fact that the bones had been deep underwater for thousands of years. That seems like a noteworthy omission.

1. James C. Chatters, Douglas J. Kennett, Yemane Asmerom, Brian M. Kemp, Victor Polyak, Alberto Nava Blank, Patricia A. Beddows, Eduard Reinhardt, Joaquin Arroyo-Cabrales, Deborah A. Bolnick, Ripan S. Malhi, Brendan J. Culleton, Pilar Luna Erreguerena, Dominique Rissolo, Shanti Morell-Hart, and Thomas W. Stafford Jr. (2014). Late Pleistocene Human Skeleton and mtDNA Link Paleoamericans and Modern Native Americans. Science 344: 750-754.

2. Prufer, Kay and Matthias Meyer (2015). Comment on "Late Pleistocene Human Skeleton and mtDNA Link Paleoamericans and Modern Native Americans." Science 347:835-a.

3. Brian M. Kemp, John Lindo, Deborah A. Bolnick, Ripan S. Malhi, and James C. Chatters (2015). Response to Comment on "Late Pleistocene Human Skeleton and mtDNA Link Paleoamericans and Modern Native Americans." Science 347:835-b.

Web page update

I updated and, I hope, improved my webpage. Please let me know if you like it, or not, or if you find any broken links or errors in it.

I am particularly interested in comments on my new page "Guide to Archaeology Resources and Journals in the Library". Both criticism and suggestions (as well as praise, of course) are all equally welcome!

Thanks!

Great science writing II: Popcorn

Here is the first of my promised posts on scientific writing.

First line: "Popcorn is the funniest corn to cook, because it jumps and makes a 'pop' sound in our pans."

Virot, Emannuel and Alexandre Ponomarenko (2015). Popcorn: Critical Temperature, Jump, and Sound. Journal of the Royal Society: Interface 12:20141247. http://dx.doi.org/10.1098/rsif.2014.1247

Enjoy!

Great Science Writing: Introduction

Some years ago, in these pages, I wrote about "the problem with science writing." Here is an excerpt from my rant.

The Best of the Best American Science Writing was a disappointment. The book is a compilation of the essays from previously published collections of essays from the annual series The Best American Science Writing 2006, 2007, etc. As I read this book, I couldn't help but think, "When did the term 'science writing' come to mean dumbed-down human-interest features journalism about science?" With the exception of a few essays, such as Ernst Mayr's, almost all the stories were mere pablum, and in my opinion some were not even well written while others were wrong or, sadly, even anti-scientific. The scientific content of most of the essays was almost nil, and I don't think I have a blinkered view of what constitutes science. Forgive me for being old fashioned or narrow-minded, but I still think of "science writing" as reports or commentaries by scientists about original research. The current belief that actual scientific discourse is unreadable and needs to translated into some other genre is both false and deleterious because it deprives society of direct access to critical information and ideas. It is false because many scientists can write well and exert great effort to communicate clearly and creatively. So there isn't any need for translators who dumb stuff down. The portrait of the scientist as illiterate is as false as any stereotype. The average scientist is probably an average writer, and since science is an international collaboration, many scientists who publish in English are writing in a second language, which doesn't make for great prose. In addition, good writing is not usually a key criterion for publication in science journals. Nevertheless, hundreds of thousands of original scientific articles are published each year, and in that thick forest there are many beautiful trees: well-written, interesting, and intellectually significant essays.

So, I was delighted to see a note in the journal Nature calling for beautiful scientific prose. The note is actually about a discussion surrounding a blog post on the topic, but still...better than a Tweet on the same subject.

The blog post, by biologist Stephen Heard, is actually in two parts. Part I is here and Part II, here. In the first part, he excerpts and discusses some of Nabokov's (yes, that Nabokov) scientific writings--he was a lepidopterist.

Heard starts by saying,

I have been wanting to start a new series here on my blog about examples of great writing in scientific publications.  There is a lot out there on great science writing.  But that is not what I am writing about here.  I mean actual scientific research papers where the writing itself is exceptional. 

I couldn't agree more. I discovered, after a little digging, that Heard also published a paper on this topic in Ideas in Ecology and Evolution (Vol. 7, No. 1, pp. 64-72) entitled "On whimsy, jokes, and beauty: can scientific writing be enjoyed?". Copies of the article are available online, including at the journal website. In the article, as in the blog posts, Heard argues that beauty and humor can recruit readers to a text and encourage them to read the whole. He recommends writing clearly but "with occasional nuggets of playfulness or glints of beauty."

While I agree with most of what he wrote, I think there is a stronger form of his theorem, if you will. Beautiful, metaphorical, and even humorous writing are modes of communication. I would argue that the use of a variety of tropes, including metaphors, similes, and even symbolism can actually improve the effectiveness of communication. So, playfulness, beauty, and humor need not be mere ornaments placed to adorn boring prose to relieve the reader's tedium; they can be, and in some cases, should be, essential elements of the rhetoric.

Let me offer just one example, from  "Disintegration of Uranium by Neutrons: A New Type of Nuclear Reaction" by Lise Meitner and O. R. Frisch (Nature Vol. 143, pp. 239-240, 1939). The article is the first report of nuclear fission, or perhaps it would be truer to say that it is the first correct explanation of the then newly observed phenomenon of nuclear fission. Meitner was a distinguished Austrian physicist who was only the second woman to receive a doctorate in physics from the University of Vienna. One of her collaborators received a Nobel prize for their work on fission, but she was overlooked.

On account of their close packing and strong energy exchange, the particles in a heavy nucleus would be expected to move in a collective way which has some resemblance to the movement of a liquid drop. If the movement is made sufficiently violent by adding energy, such a drop may divide itself into two smaller drops.
    In the discussion of the energies involved in the deformation of nuclei, the concept of surface tension of nuclear matter has been used and its value has been estimated from from simple considerations regarding nuclear forces. It must be remembered, however, that the surface tension of a charged droplet is diminished by its charge, and a rough estimate shows that he surface tension of nuclei, decreasing with increasing nuclear charge, may become zero for atomic numbers of the order of 100 (Meitner and Frisch 1939:239).

It seems to me that the use of the metaphor of a "drop," while highly evocative, is not merely an ornamental flourish. Rather, it is very precisely employed by Meitner to describe and envisage the phenomenon; moreover, it is used productively to explain and communicate the character of the phenomenon by analogy. Note that the comparison of an atomic nucleus to a droplet of liquid is not literally true: Meitner used a metaphor. A metaphor is rhetorical device, not an objective description.

So, even in this very staid physics article from 1939, which in general is written in the most conventional style, we witness the use of rhetorical devices to aid the reader's comprehension. I assert that metaphors, as well as allied rhetorical devices and tropes, are actually part of the traditional armament that scientists deploy in their writing. One could delve into the linguistics literature on metaphor to prove the significance as well as the ubiquity of metaphor in communication, but I hope that is not necessary.

I should say that I chose this article somewhat at random. It's obviously a very important article--it reports the discovery of nuclear fusion, after all--and presumably it is well-known to physicists, but less so to archaeologists like me.

The traditional ideal of scientific writing elevates clarity above all else, and uses simplicity to achieve clarity. But it also pretends to objectivity and authority. Guides to science writing, amazingly, still argue for the use of passive and neutral constructions to create the illusion of objectivity and authority. Saying "the reagent was added to the solution" is supposed to convey objectivity and authority, as opposed to the more natural and honest "I added the reagent to the solution." I think that using the first person and the active voice is clearer and more honest than a rhetorical pretense of authority. Authority comes from honesty and truth; it does not need to be dressed up and paraded out in an awkward voice. A scientist's first duty is to truth, and that trumps style. If the truth is that the reagent was added by an undergraduate who blew up the lab twice before he got it right, then that should be so stated.

I plan to occasionally post scientific articles with interesting prose to remind us of what we can, and perhaps should, be doing.

Archaeology: The Ideal Liberal Education

I've long thought that archaeology has the potential to offer students an ideal liberal education. Consider this:

• archaeology is a social science, so to be an archaeologist, you need to know something about society, social theory, and human behavior. 
• archaeology is also one of the humanities because it is a historical science, so a student needs to know something about history too.
• archaeology is a natural science as well, so you need to know about the scientific method, research design, sampling, and hypothesis testing to carry out research.
• archaeology has a significant mathematical component: we use statistics constantly, but we also use geometry, for example, when we make maps, which we do all the time. Spatial analysis, seriation, design analysis, and many other tasks we perform require mathematics more than statistics. 
• archaeological science includes forays into chemistry, physics, and a host of allied fields in the natural and applied sciences.
• zooarchaeology and paleoethnobotany require a knowledge of the natural environment in general as well as the specifics of zoology and botany.
• archaeologists use their knowledge of soils and geomorphology to find sites and understand their development and structure.
• archaeologists study the paleoclimate and the paleoenvironment, which obviously requires some understanding of those fields, including a dose of isotope chemistry.
• archaeologists study geology not only to understand soils and geomorphology but also to find sources of raw materials, such as chert, obsidian, potting clay, marble, metals, and so forth.
• epigraphy is the branch of archaeology dedicated to the study of inscriptions; inscriptions are texts, with all that implies for textual analysis and hermeneutics.
• archaeologists study art: we study art history and we analyze the style of artifacts.
• archaeologists study architecture--mostly from the perspective of architectural history but sometimes from an engineering perspective as well.
• archaeologists must learn how to write well because the final product of any archaeological research is not a pile of artifacts or a bag of soil samples, but rather a report, article, or monograph.
• archaeologists have to learn to play well with others. Archaeology is a collaborative undertaking: we never work alone. This requires interpersonal skills and often managerial ability--if you're in charge.
• archaeology requires meticulous work but also a broad, integrative vision that allows one to synthesize ideas from all these different fields.

I am delighted to find I am not the first person to come to this conclusion.

From another point of view the subject [archaeology] should be considered; it gives a more truly “liberal education” than any other subject, as presently taught. A complete archaeological training would require a full knowledge of history and art, a fair use of languages, and a working familiarity with many sciences. The one-sided growth of modern training, which produces a B.A. who knows nothing of natural science, or else a B.Sc. who knows nothing of human nature, is assuredly not the ideal for a reasonable man. Archaeology,—the knowledge of how man has acquired his present position and powers—is one of the widest studies, best fitted to the open mind, and to produce that type of wide interests and toleration which is the highest result of education.

Sir W. M. Flinders Petrie (1904). Methods & Aims in Archaeology. London: Macmillan and Co., p. viii.

Flinders Petrie was an Egyptologist of great distinction and was arguably something of a polymath himself. Note the description of the two cultures, over 50 years before C. P. Snow would formalize the idea.

Archaeologists have not made much of an effort to promote their field, particularly at the undergraduate level, as the paragon of a liberal education, or as anything else. We remain a small field, content with the few students who are really interested in being archaeologists. Meanwhile,  large departments prepare hoards of students in Communications, Business, Political Science, and Criminal Justice. I hope there are strong job markets in those fields because I would hate to think that those students are not finding jobs. We should remember that an American undergraduate education is designed as a general liberal education, not primarily as pre-professional training.

Today we witness policy makers and politicians pushing for increased STEM education. They usually hawk their prescriptions as engines of innovation, entrepreneurship, and job creation. Anyone who believes this does not have a very realistic or accurate view of either education or business. Success in business, whether as an employee or an entrepreneur, requires a broad range of skills from a variety of disciplines, including the humanities, sciences, and social sciences. Studying STEM fields alone is not an effective or efficient way of promoting innovation or entrepreneurship. Real innovation requires an understanding of society, psychology, aesthetics, and other matters that you will not find in mathematics, engineering, and physics classes. Walter Isaacson makes this case persuasively, albeit anecdotally, in his recent book The Innovators.

I have no doubt that experts in many disciplines will claim that their fields are as broad as archaeology. A few other fields probably are, but they are the exception rather than the rule. Archaeology remains a distinct anomaly, which is also why archaeologists are usually scattered among multiple departments at most American universities. That is probably one reason we have difficulty promoting our discipline as anything in particular, much less the great liberal education it truly can be.

"Be like the Soil:" It's the International Year of Soils

The Food and Agriculture Organization of the United Nations has declared 2015 the International Year of Soils. Both Science and Nature have published editorials decrying the rapid destruction and contamination of soils and calling for more research.

To started celebrating the Year of Soil, I post here the text of a beautiful little talk on the subject by Dr. Timothy Beach.

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Tim Beach, Tropaia Lecture 2014 (5-17-2014) School of Foreign Service Professor of the Year 2014 You and I are only “temporarily not soil” [1] A few years ago, I was the season’s first scientist under the steaming canopy of our rainforest study site. This meant shoring up the trail and bridges, and accepting a lower place on the food chain. This requires sharp focus: the rainforest is a beautiful but risky place: you keep your eyes wide open and make sure you are not the slowest in the group. While clearing the trail, I noticed the distinct tracks of an endangered tapir, the largest land mammal in the Neotropics. Then, I saw an even rarer track: a jaguar, the world’s third largest cat. My research goal here has been to study soil with the intent to understand water, ecosystems, human interactions, and climate change. These may seem more  mundane, but to the scientist’s eye are as thrilling as happening into the midst of a food chain  unconcerned with your life. Continuing with food chains, I want to thank my students, colleagues, and mentors, who have taught me in equal parts. I also congratulate all the 2014 honorees who have worked so diligently. You have honed your minds and skills and have considered deeply under the seeds tended so well by many great teachers, including many on this stage as worthy of any teaching awards. I represent a new trend in this venerated school athwart the Potomac and the Piedmont: indeed Something New under the Sun [2] of the SFS: a scientist, a student of nature, and a physical geographer; these were all firsts, and for the betterment of this fine School, the camel’s nose is under this tent; I shall soon be eclipsed. We stand here on precious ground, because of the School of Foreign Service, where so many have gone before to speak to the world and learn of the world. But to geoscientists, this ground rings with Hoya Saxa [3] or what rocks of our firmament that once lay bestride Africa and Scotland in the super continent of Pangaea. These plates rifted apart one fifth of the way around the Earth over 200 million years to form a precipice that now sends its promise of hope and education to all those far flung provinces of former Pangaea. This living, moving, breathing Earth is the only place where we know life can exist in the Universe and where the perfect conditions found the only being that could arrive to “know this place for the first time.” [4] I have spent my career studying and teaching about this verdant and oblate spheroid, here on this erstwhile edge of Africa. The ceaseless work, not to mention circumnavigating the earth twice by foot and bike, have left little time to despair the litany of losses of our unique planet and the quickened pace of global wierding. But I have taught all of these and fear the loss of what we did not discover from these natural archives that might have made life better for all. When I came to Georgetown, a generation ago, my charge was to teach Environmental Science, and I was hungry for knowledge and to comprehend Nature. I have had the privilege to teach a score of new courses from climate, to water, to soils and agriculture, to geoscience, to environmental restoration, and more. My creed shared with my STIA colleague Chuck Weiss was Carl Sagan’s still unfortunately fitting phrase: “We live in a society exquisitely dependent on science and technology, in which hardly anyone knows anything about science and technology.” [5] My obligation was to remedy this in classrooms, labs, and the field, and to help build a faculty. Geoscience and ecology begin and end in the field, but they also provide the transcendent satisfaction of knowing your place, from the soil mycorrhiza to Mahogany trees to the 65 million year old rocks formed by the meteorite that doomed the dinosaurs. “For always roaming with a hungry heart,” [6] I have taken hundreds of students to 6 countries to give them this experience and pass along what my best teachers gave me. The privilege of teaching students is equaled only by creating new knowledge and knowing Nature in intimate detail. “Nature is always more subtle, more intricate, more elegant than what we are able to imagine.” Soil is at the core of all of my work. “What I stand for is what I stand on.” [7] If science is the most precious thing, [8] then soil is the most precious science, the ultimate combination of all Earth’s spheres. As the great poet says: “be like the soil.” [9] Soil is the most diverse ecosystem. But it is a humble one, like serious wine: you have to learn to appreciate it. The soil is our ultimate ecosystem service, which are nature’s free gifts “we could not make them and we could not live without then.”  [10] Soil gives us a firm foundation, fertility, antibiotics, water purification, carbon storage and waste breakdown, and a mind boggling array of food webs that cycle nutrients and maintain the soil’s  political equilibria. A scientist recently studied polluted rain water filtering through a Canadian soil and found that it became completely clean through a myriad of still little known processes. [11] I also come with a fascination and devotion to international affairs and a world of places. From this perspective, there are no aspects of international affairs that do not include science. A clear example of this is atmospheric carbon, our greatest challenge because “it is hitched to everything else in the Universe” [12], and will stay relevant to us for the rest of our lives. There are no easy fixes, but the soil can pull carbon out of the air, and thereby make soils more fertile and able to purify water, and indeed soil stores about 4 times more carbon than the air. This will be a focus of the next stage my career.  “And to make an end, is also a beginning.” [13] This earth that has evolved through eons of risk is now in the Anthropocene, this brave new world [14] when humans have altered it so much that like the Pottery Barn analogy: we now own it (though it is far from completely broken). We now hold the fate of the tapirs, the jaguars, and the climate. And more of international affairs will be about the loss of ecosystems and their trillion dollar free services, and we will have to rise to better manage this only place where we know life has ever existed. This implies nurture, firm foundations, capturing carbon, purifying water, and maintaining diverse life and ecosystem equlibria. In other words, international affairs must inevitably “Be like the soil.” Thanks and congratulations!  1 “temporarily not soil” is what the soil scientist Francis Hole meant by appending TNS to his  signature  (http://www.secfac.wisc.edu/senate/2002/0506/1640(mem_res).pdf) 2 “Something New under the Sun” is the title of a book by J.R. McNeill (2001) that refers to Ecclesiastes  1:4-11:“There is nothing new under the sun,” which is a common quote. 3 Hoya Saxa means what rocks and is a motto of Georgetown University 4 T. S. Eliot, 1945. Little Gidding, part V. 5 Carl Sagan, 1990. Why We Need To Understand Science, The Skeptical Inquirer Vol. 14.3. 6 Alfred Tennyson, 1833. Ulysses. 7 Wendell Berry, 1980. Below, a poem in A Part. Berkeley, CA: North Point Press. 8 Carl Sagan, 1995. Demon Haunted World; the first chapter is titled The Most Precious Thing, referring to science. 9 Rumi’s Seven Advices: “In modesty and humility, be like the soil.” 10 Wendell Berry, stated similar things in several interviews (see p. 15 in https://www.heartwood.org/heartbeat/Spring_2011.pdf) 11 William Shotyk, 2013. “Peat bogs and their organic soils: Archives of atmospheric change and  global environmental significance” (Philippe Duchaufour Medal Lecture). EGU 4-9-2013, Vienna,  Austria. 12 John Muir, 1911. My First Summer in the Sierra, Boston: Houghton Mifflin, p. 110. 13 T.S. Eliot, 1945. Little Gidding, part V. 14 Shakespeare, 1611. The Tempest, Act V, Scene I.

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(N.B.: I had to reformat the text from a portable document, and I may have thereby introduced errors. CTB)

Thanks, Tim!

Tim Beach in Nicaragua